Variant report

Variant	rs12504088
Chromosome Location	chr4:106662004-106662005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10019217	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10049527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10516522	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11722731	0.86[YRI][hapmap]
rs11930244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11930965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11936611	0.87[ASN][1000 genomes]
rs11942577	1.00[CHB][hapmap]
rs12511885	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512339	0.86[ASN][1000 genomes]
rs13110070	0.81[ASN][1000 genomes]
rs17036093	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17036097	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17036102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17036158	0.97[ASN][1000 genomes]
rs17036254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2193852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2193853	0.97[ASN][1000 genomes]
rs2193854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs28370551	0.95[ASN][1000 genomes]
rs28391170	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28450989	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28559909	0.92[ASN][1000 genomes]
rs28698939	0.81[ASN][1000 genomes]
rs3796926	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4235415	0.83[ASN][1000 genomes]
rs4490460	0.95[ASN][1000 genomes]
rs4698950	0.88[ASN][1000 genomes]
rs4698951	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4699192	0.81[ASN][1000 genomes]
rs4699193	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4699194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4699195	0.95[ASN][1000 genomes]
rs4699197	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4699198	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs58388061	1.00[ASN][1000 genomes]
rs59961848	0.90[ASN][1000 genomes]
rs60774107	0.92[ASN][1000 genomes]
rs60861135	0.97[ASN][1000 genomes]
rs6817029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6820671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6825379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6826631	0.87[ASN][1000 genomes]
rs6829915	0.81[ASN][1000 genomes]
rs6843771	0.87[ASN][1000 genomes]
rs7658055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7659526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7665588	0.97[ASN][1000 genomes]
rs7696836	0.81[ASN][1000 genomes]
rs7697619	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv879700	chr4:106643445-106745057	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1000947	chr4:106651153-106701679	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12504088	SPTLC2	trans	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106631000-106663000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr4:106631000-106669400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr4:106634000-106693200	Weak transcription	K562	blood
4	chr4:106635600-106665000	Weak transcription	HUVEC	blood vessel
5	chr4:106635600-106669800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:106643000-106662600	Weak transcription	Fetal Kidney	kidney
7	chr4:106648000-106669800	Weak transcription	HSMM	muscle
8	chr4:106657000-106662400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:106657000-106663000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:106657000-106669800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:106657000-106669800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:106657000-106670000	Weak transcription	Gastric	stomach
13	chr4:106657000-106670200	Weak transcription	Ovary	ovary
14	chr4:106659000-106669800	Weak transcription	Dnd41	blood
15	chr4:106659200-106663000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:106659200-106666800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr4:106659200-106667200	Weak transcription	A549	lung
18	chr4:106659200-106669800	Weak transcription	Left Ventricle	heart
19	chr4:106659400-106662200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:106659400-106662400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:106659400-106662800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:106659400-106663600	Weak transcription	Aorta	Aorta
23	chr4:106659400-106664800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:106659400-106668600	Weak transcription	Primary T cells from cord blood	blood
25	chr4:106659400-106679400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:106659400-106686400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:106659600-106662800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:106659600-106665200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr4:106659600-106666400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:106659600-106666600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:106659600-106668400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr4:106659600-106669400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:106659600-106670000	Weak transcription	Fetal Intestine Large	intestine
34	chr4:106659600-106671000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:106659600-106691800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:106659800-106662400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr4:106659800-106662400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr4:106659800-106669600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr4:106659800-106671800	Weak transcription	Fetal Brain Female	brain
40	chr4:106660000-106665200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:106660000-106670200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:106660200-106667800	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:106660200-106670000	Weak transcription	Adipose Nuclei	Adipose
44	chr4:106660200-106671200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:106660600-106665000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr4:106660800-106669800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:106661400-106663000	Weak transcription	Fetal Stomach	stomach
48	chr4:106661400-106663000	Weak transcription	Pancreas	Pancrea
49	chr4:106661400-106665000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:106661400-106669000	Weak transcription	Spleen	Spleen

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